As a test-bed for China reform，Shanghai Pilot Free Trade Zone proposed to develop headquarters economy as one of the overall goal. Shanghai Pilot Free Trade Zone will become an important area to attract the regional headquarters of multinational companies. On the current situation，there is still a considerable gap between the environment of developing regional headquarters in Shanghai Pilot Free Trade Zone and Other internationalization mature City. So Shanghai Pilot Free Trade Zone must learn the development experience of mature markets and international cities in order to achieve efficient，leap-forward development. In Asia，the city of the most significant headquarters economy effect is undoubtedly Hong Kong. This paper selects the factors affecting the regional headquarters choosing location，and compares and analyzes these factors in both Shanghai Pilot Free Trade Zone and Hong Kong. Finally，provide empirical reference to development of headquarters economy in Shanghai Pilot Free Trade Zone in according to certain gap of developing headquarters economy.